The molybdenum storage protein (MoSto) can store more than 100 Mo or W atoms as discrete polyoxometalate (POM) clusters. Here, we describe the three POM cluster sites along the threefold axis of the protein complex based on four X-ray structures with slightly different polyoxomolybdate compositions between 1.35 and 2 angstrom resolution. In contrast to the Mo alpha-out binding site occupied by an Mo-3 cluster, the Mo alpha-in and Mo-beta binding sites contain rather weak and non-uniform electron density for the Mo atoms (but clearly identifiable by anomalous data), suggesting the presence of POM cluster ensembles and/or degradation products of larger aggregates. The "Mo alpha-in cluster ensemble" was interpreted as an antiprism-like Mo-6 species superimposed with an Mo-7 pyramide and the "Mo-beta cluster ensemble" as an Mo-13 cluster (present mostly ins degraded form) composed of a pyramidal Mo-7 and a Mo-3 building block linked by three spatially separated MoOx units. Inside the ball-shaped Mo-13 cluster sits an occluded central atom, perhaps a metal ion. POM cluster formation at the Mo alpha-in, and Mo-beta sites appears to be driven by filtering out and binding/protecting self-assembled transient species complementary to the protein template. (C) 2014 Elsevier Inc. All rights reserved.